rs1263173

Variant names:

• chr11-116810292-G-A
• rs1263173

Your query was ambiguous. Multiple possible variants found:

• chr11-116810292-G-A
• chr11-116810292-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.529 in 152,098 control chromosomes in the GnomAD database, including 25,071 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (25071 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878
• Publications: 37 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80503 AN: 151980 Hom.: 25075 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.564

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.529 AC: 80504 AN: 152098 Hom.: 25071 Cov.: 33 AF XY: 0.520 AC XY: 38646 AN XY: 74344

African (AFR) AF: 0.209 AC: 8660 AN: 41468

American (AMR) AF: 0.561 AC: 8564 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1533 AN: 5180

South Asian (SAS) AF: 0.439 AC: 2115 AN: 4814

European-Finnish (FIN) AF: 0.595 AC: 6301 AN: 10582

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49035 AN: 67988

Other (OTH) AF: 0.558 AC: 1180 AN: 2114

Alfa AF: 0.649 Hom.: 106431

Bravo AF: 0.517

Asia WGS AF: 0.337 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.45
PhyloP100		0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1263173; hg19: chr11-116681008;